Odds are you sometimes think about calories. They are among the most often counted things in the universe. When the calorie was originally conceived it was in the context of human work. More calories meant more capacity for work, more chemical fire with which to get the job done, coal in the human stove. Fat, it has been estimated, has nine calories per gram, whereas carbohydrates and proteins have just four; fiber is sometimes counted separately and gets awarded a piddling two. Every box of every food you have ever bought is labeled based on these estimates; too bad then that they are so often wrong.

A Food is Not a Food—Estimates of the number of calories in different kinds of foods measure the average number of calories we could get from those foods based only on the proportions of fat, carbohydrates, protein and sometimes fiber they contain (In essence, calories ingested minus calories egested). A variety of standard systems exist, all of which derive from the original developed by Wilbur Atwater more than a hundred years ago. They are all systems of averages. No food is average.

Differences exist even within a given kind of food. Take, for example, cooked vegetables. Cell walls in some plants are tougher to break down than those in others; nature, of course, varies in everything. If the plant material we eat has more of its cell walls broken down we get more calories from it. In some plants, cooking ruptures most cell walls; in others, such as cassava, cell walls hold strong and hoard their precious calories in such a way that many of them pass through our bodies intact.

It is not just cooked vegetables though. Nuts flagrantly do their own thing, which might be expected given that nuts are really seeds whose mothers are invested in having them escape digestion. Peanuts, pistachios and almonds all seem to be less completely digested than their levels of protein, fat, carbohydrates and fiber would suggest. How much? Just this month, a new study by Janet Novotny and colleagues at the USDA found that when the “average” person eats almonds she receives just 128 calories per serving rather than the 170 calories “on the label.”

It is not totally clear why nuts such as almonds or pistachios yield fewer calories than they “should.” Tough cell walls? Maybe. But there are other options too, if not for the nuts themselves then for other foods.

For one, our bodies seem to expend different quantities of energy to deal with different kinds of food (the energy expended produces heat and so is referred to by scientists as “diet-induced thermogensis”); some foods require us to do more work than others. Proteins can require ten to twenty times as much heat-energy to digest as fats, but the loss of calories as heat energy is not accounted for at all on packaging.

For another, foods differ in how and where they are digested in our guts. Some foods such as honey are so readily used that our digestive system is really not even put to good use. They are absorbed in our small intestines; game mostly over. More complex foods, on the other hand, such as cassava or almonds, have to travel to the colon where they meet up with the largest concentrations of our little friends, the microbes. Digestion continues with the help of our trillions of microbes but nutrients are shared between us and them. The microbes help to break down many compounds our own bodies cannot and in doing so go on to produce a mix of more microbes, gases (such as methane) and then fatty acids. The accounting associated with this process of sharing with the microbes is not considered in calorie counting.

Finally, some foods require our immune system to get involved during digestion in order to deal with potential pathogens. No one has evaluated very seriously just how many calories this might involve, but it might be quite a few. A somewhat raw piece of meat can have lots of interesting species for our immune systems to deal with. Even if our immune system does not attack any of the species in our food it uses energy to take the first step of distinguishing good from bad.

So much is different between the fate of different foods that it is almost certainly rare that the estimate of the number of calories in a food and the true number correspond well. And we haven’t even gotten to the biggest way in which a calorie is not always a calorie, processing.

In a paper published recently in the Proceedings of the National Academy of the Sciences, Rachel Carmody and collaborators at Harvard University examined the effect of the two most ancient forms of food processing–cooking and grinding (technically in their study, pounding)–on the calories available in those same foods.

Carmody knew from her previous work that starches like those in sweet potatoes have more of their calories available to digestion the more they are cooked (at least to a point). As a result, no two sweet potatoes you cook will ever have the exact same number of calories because they grew differently and because you will have cooked them slightly differently. But what, Carmody wondered, about meat? Meat is relatively easily digested; its calories might be just as available in sushi as in a McDonald’s hamburger. Surely, meat is just meat, the one thing that our estimates of calories get right. Wrong.

Digestion is difficult to study. It is hard to make participants, even college students, eat, say, nothing but raw beef for several days. Carmody and her colleagues circumvented this problem by studying mice; they monitored the weight of mice fed different diets. The mice are secretive about their digestion too though so Carmody measured how the mice moved and how much weight they gained as a measure of the amount of energy that was not being lost through inefficiency as feces. All things equal, the bigger the mice got on a given diet, the more calories they were getting. Carmody fed adult, male mice organic sweet potatoes (to, in essence, retest what was already known) or organic, lean beef. These foods were served up raw and whole, raw and pounded, cooked and whole, or cooked and pounded. The standard system of calories, the one used to put the numbers on the food you buy in the store, assumes (and hence also predicts) these have no effect on calorie content; but would they? The mice were allowed to eat as much as they wanted and how much they consumed was closely monitored (Carmody had to pick each and every bit of uneaten food up from inside the cage).

The mice on the different diets got about the same amount of exercise. They all had a wheel to run on, and they did not differ one treatment to the next in terms of how inclined they were to take a jog. They did differ, however, in how much they weighed at the end of the study. As predicted, mice lost more than four grams of weight on raw sweet potatoes, but gained weight when given cooked sweet potatoes (whether or not they were pounded). But what about meat? Cooked meat was easier to digest. The mice lost 2 grams of body mass on raw meat but just 1 gram on cooked meat. In retrospect this does not seem surprising. Heat denatures proteins and makes them easier to digest. Heat also kills bacteria and might decrease the immune cost of eating meat by reducing the work the immune system has to do which allows the body to make, well, more body for a given number of calories.

In general, it seems that the more processed foods are the more they actually give us the number of calories we see on the box, bag or other sort of label. This applies not just to cooking and pounding but also to industrial processing. A new study this year found that in a lab experiment individual humans who ate 600 or 800 calorie portions of whole wheat bread (with nuts and seeds on it) and cheddar cheese actually expended twice as much energy, yes twice, in digesting that food as did individuals who consumed the same quantity of white bread and “processed cheese product.” As a consequence, the net number of calories the whole food eaters received was ten percent less than the number received by the processed food eaters (because they spent some of their calories during digestion). Similar work in pythons has shown that cooked and/or ground up meat also requires less energy to digest (at least for pythons). If you want more calories, whether or not you are a snake, cook, pound and otherwise predigest your food.

A Body is Not a Body—Amazingly, there are more ways in which a calorie is not a calorie. Even if two people were to somehow eat the same sweet potato cooked the same way they would not get the same number of calories. Carmody and colleagues studied a single strain of heavily inbred lab mice such that their mice were as similar to each other as possible. Yet the mice still varied in terms of how much they grew or shrank on a given diet, thanks presumably to subtle differences in their behavior or bodies. Humans vary in nearly all traits, whether height, skin color, or our guts. Back when it was the craze to measure such variety European scientists discovered that Russian intestines are about five feet longer than those of, say, Italians. This means that those Russians eating the same amount of food as the Italians likely get more out of it. Just why the Russians had (or have) longer intestines is an open question. Surely other peoples differ in their intestines too; intestines need more study, though I am not going to volunteer to do the dirty work. We also vary in terms of how much of particular enzymes we produce; the descendents of peoples who consumed lots of starchy food tend to produce more amylase, the enzyme that breaks down starch. Then there is the enzyme our bodies use to digest the lactose in milk, lactase. Many (some say most) adults are lactose deficient; they do not produce lactase and so do not break down the lactose in milk. As a result, even if they drink milk they receive far fewer calories from doing so than do individuals who produce lactase. Each of us gets a different number of calories out of identical foods because of who we are and who our ancestors were.

A Microbe is Not a Microbe—Finally, a magically real new literature considers the microbes in and on human bodies. We have known for years that we are covered in microbes and they matter (a lot), but only recently has the study of these microbes become cool, thanks in part to new tools. Lynn Margulis was arguing in the late 1960s that organisms were nearly all engaged in symbioses that defined who they were. The broader biological literature has now caught on to her wild insight and renamed it, but that doesn’t mean studying human symbionts is easy. Margulis studied the symbionts of protists and termites (what we now call their microbiomes). She could look at the symbionts of the protists when they were still alive and she could cut open the termites (Which she did hundreds of times; it was one of her greatest joys.). With humans, studies of symbionts usually involve fecal samples, which is a bit like studying the center of the Earth by looking at lava, if, I guess, the lava were feces. Something of the grandeur is missed. The recent literature on human symbionts is wondrous but still groping at the edge of understanding. Scientists study the microbes in the feces from twelve white dudes from New Jersey and make an announcement about the entirety of humanity. One would be reasonable to be suspicious of anyone claiming to have understood the simple truths of the microbes in our guts.

Nonetheless, differences among individual humans in their symbionts do seem to make differences in how they digest food—individuals appear to differ in their metabolism depending on just which microbes they have. In addition, some microbes are found only in particular peoples where they appear to play a unique role. In some Japanese populations there exists a gut microbe that has stolen genes from a marine bacterium; those genes help the bacterium to break down seaweed (such as that encountered in sushi rolls). How you digest food depends on which microbes you have and which microbes you have differs from one person to the next. Different foods can both affect and be affected by our microbes. Hunter-gatherer diets in the southwestern U.S. once abounded in compounds our bodies are unable to digest but that are readily digested by microbes. Conversely, many modern diets provide very little good food for microbes, very likely to our detriment. Microbes seem likely to suffer on a diet of cheese product and white bread because both are used up by the time they make it to the colon. Margulis would have predicted all of this forty years ago based on termites (We seem to more easily accept mice as models of our bodies than we do termites). But the point is that your microbes are different than mine which likely matters to digestion; we just can’t yet really clearly say how.

A Calorie is Not a Calorie—When all is said and done the good news is we have figured how to make and eat foods in which the calories are maximally available. We process them. We cook them. We ferment them. We cook them again until they actually give us as many calories as the box says. It has been plausibly argued (by quite a number of reasonable researchers at this point) that what made our early human diet unique was cooking and that cooking, in turn, allowed for some morphological changes in our bodies (bigger brains, relatively smaller guts) along with many societal changes. Our ancestors may have combined a preference for cooked food with the unique ability to make it on demand. The mice in Carmody’s study, interestingly, not only got more energy out of cooked meat, they also preferred it. But for as much as they like grilled steak, they will never invent cooking. We did. If this idea is right, what we inherit as our unique recent history is not the need for some specific amount of meat or fat but instead the preference for as many calories as we can get as quickly as we can get them so that we might have leisure time to invent, organize, and text each other.

It is a testament to human ingenuity that we have now figured out how to provide as many calories as possible in our foods. We don’t even really need for our intestines to do much work, our bacteria either, or even our teeth for that matter. Our modern diets are a measure of our evolutionary success, or at least they would be from the perspective of our paleo ancestors who needed and wanted excess calories. They are not successes from our modern perspective. We now have too many calories and too many of those calories are of low quality. One in three Americans is now obese. Over the last thirty years the number of calories we eat has increased, but so has the number of those calories that come from highly processed foods. In this light, we would do well to eat fewer processed foods and more raw ones. This is not a novel insight (Such foods, after all, tend to have more nutrients such as B vitamins, phytonutrients and minerals and so are good for reasons having nothing to do with counting calories). But what might be novel is the realization that in eating such foods you could lose weight while keeping the precise tally of the calories you consume exactly the same. Of course how much weight you lose depends on who you and your microbes are.

About the Author: Rob Dunn is a science writer and biologist in the Department of Biology at North Carolina State University. His first book, Every Living Thing, told the stories of the sometimes obsessive, occasionally mad, and always determined, biologists who have sought to discover the limits of the living world. His new book, The Wild Life of Our Bodies, explores how changes in our interactions with other species, be they the bacteria on our skin, forehead mites or tigers, have affected our health and well being. Rob lives in Raleigh, North Carolina with his wife, two children, and lots of microbes. Follow on Twitter @RobRDunn.